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Ge L, Shi X, Li B, Gong K. Fluctuation-induced dispersion forces on thin DNA films. Phys Rev E 2023; 107:064402. [PMID: 37464699 DOI: 10.1103/physreve.107.064402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/15/2023] [Indexed: 07/20/2023]
Abstract
In this work, the calculation of Casimir forces across thin DNA films is carried out based on the Lifshitz theory. The variations of Casimir forces due to the DNA thicknesses, volume fractions of containing water, covering media, and substrates are investigated. For a DNA film suspended in air or water, the Casimir force is attractive, and its magnitude increases with decreasing thickness of DNA films and the water volume fraction. For DNA films deposited on a dielectric (silica) substrate, the Casimir force is attractive for the air environment. However, the Casimir force shows unusual features in a water environment. Under specific conditions, switching sign of the Casimir force from attractive to repulsive can be achieved by increasing the DNA-film thickness. Finally, the Casimir force for DNA films deposited on a metallic substrate is investigated. The Casimir force is dominated by the repulsive interactions at a small DNA-film thickness for both the air and water environments. In a water environment, the Casimir force turns out to be attractive for a large DNA-film thickness, and a stable Casimir equilibrium can be found. The influences of electrolyte screening on the Casimir pressure of DNA films are also discussed at the end. In addition to the adhesion stability, our finding could be applicable to the problems of condensation and decondensation of DNA, due to fluctuation-induced dispersion forces.
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Affiliation(s)
- Lixin Ge
- School of Physics and Electronic Engineering, Xinyang Normal University, Xinyang 464000, China
| | - Xi Shi
- Department of Physics, Shanghai Normal University, Shanghai 200234, China
| | - Bingzhong Li
- School of Physics and Electronic Engineering, Xinyang Normal University, Xinyang 464000, China
| | - Ke Gong
- School of Physics and Electronic Engineering, Xinyang Normal University, Xinyang 464000, China
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2
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Lima RPA, Malyshev AV. Charge transfer mechanisms in DNA at finite temperatures: From quasiballistic to anomalous subdiffusive charge transfer. Phys Rev E 2022; 106:024414. [PMID: 36109995 DOI: 10.1103/physreve.106.024414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
We address various regimes of charge transfer in DNA within the framework of the Peyrard-Bishop-Holstein model and analyze them from the standpoint of the characteristic size and timescales of the electronic and vibrational subsystems. It is demonstrated that a polaron is an unstable configuration within a broad range of temperatures and therefore polaronic contribution to the charge transport is irrelevant. We put forward an alternative fluctuation-governed charge transfer mechanism and show that the charge transfer can be quasiballistic at low temperatures, diffusive or mixed at intermediate temperatures, and subdiffusive close to the DNA denaturation transition point. Dynamic fluctuations in the vibrational subsystem is the key ingredient of our proposed mechanism which allows for explanation of all charge transfer regimes at finite temperatures. In particular, we demonstrate that in the most relevant regime of high temperatures (above the aqueous environment freezing point), the electron dynamics is completely governed by relatively slow fluctuations of the mechanical subsystem. We argue also that our proposed analysis methods and mechanisms can be relevant for the charge transfer in other organic systems, such as conjugated polymers, molecular aggregates, α-helices, etc.
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Affiliation(s)
- R P A Lima
- GISC and GFTC, Instituto de Física, Universidade Federal de Alagoas, Maceió AL 57072-970, Brazil
| | - A V Malyshev
- GISC, Departamento de Física de Materiales, Universidad Complutense, E-28040 Madrid, Spain
- Ioffe Physical-Technical Institute, St-Petersburg, Russia
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3
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Orimoto Y, Hisama K, Aoki Y. Local electronic structure analysis by ab initio elongation method: A benchmark using DNA block polymers. J Chem Phys 2022; 156:204114. [DOI: 10.1063/5.0087726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ab initio elongation (ELG) method based on a polymerization concept is a feasible way to perform linear-scaling electronic structure calculations for huge aperiodic molecules while maintaining computational accuracy. In the method, the electronic structures are sequentially elongated by repeating (1) the conversion of canonical molecular orbitals (CMOs) to region-localized MOs (RLMOs), that is, active RLMOs localized onto a region close to an attacking monomer or frozen RLMOs localized onto the remaining region, and the subsequent (2) partial self-consistent-field calculations for an interaction space composed of the active RLMOs and the attacking monomer. For each ELG process, one can obtain local CMOs for the interaction space and the corresponding local orbital energies. Local site information, such as the local highest-occupied/lowest-unoccupied MOs, can be acquired with linear-scaling efficiency by correctly including electronic effects from the frozen region. In this study, we performed a local electronic structure analysis using the ELG method for various DNA block polymers with different sequential patterns. This benchmark aimed to confirm the effectiveness of the method toward the efficient detection of a singular local electronic structure in unknown systems as a future practical application. We discussed the high-throughput efficiency of our method and proposed a strategy to detect singular electronic structures by combining with a machine learning technique.
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Affiliation(s)
- Yuuichi Orimoto
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Keisuke Hisama
- Department of Interdisciplinary Engineering Sciences, Chemistry and Materials Science, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Yuriko Aoki
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
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Adhikari P, Podgornik R, Jawad B, Ching WY. First-Principles Simulation of Dielectric Function in Biomolecules. MATERIALS (BASEL, SWITZERLAND) 2021; 14:5774. [PMID: 34640170 PMCID: PMC8510404 DOI: 10.3390/ma14195774] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/26/2021] [Accepted: 09/28/2021] [Indexed: 02/06/2023]
Abstract
The dielectric spectra of complex biomolecules reflect the molecular heterogeneity of the proteins and are particularly important for the calculations of electrostatic (Coulomb) and electrodynamic (van der Waals) interactions in protein physics. The dielectric response of the proteins can be decomposed into different components depending on the size, structure, composition, locality, and environment of the protein in general. We present a new robust simulation method anchored in rigorous ab initio quantum mechanical calculations of explicit atomistic models, without any indeterminate parameters to compute and gain insight into the dielectric spectra of small proteins under different conditions. We implement this methodology to a polypeptide RGD-4C (1FUV) in different environments, and the SD1 domain in the spike protein of SARS-COV-2. Two peaks at 5.2-5.7 eV and 14.4-15.2 eV in the dielectric absorption spectra are observed for 1FUV and SD1 in vacuum as well as in their solvated and salted models.
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Affiliation(s)
- Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (P.A.); (B.J.)
| | - Rudolf Podgornik
- School of Physical Sciences, Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (P.A.); (B.J.)
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (P.A.); (B.J.)
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Barbosa MB, Martins EMDN, Teixeira TF, Carvalho RDE, Coelho JP, Resende RR, Oliveira EF, Santos AP, Andrade ASRD, Furtado CA. A carefully designed nanoplatform based on multi walled carbon nanotube wrapped with aptamers. Colloids Surf B Biointerfaces 2018; 175:175-183. [PMID: 30530003 DOI: 10.1016/j.colsurfb.2018.11.064] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/21/2018] [Accepted: 11/26/2018] [Indexed: 02/01/2023]
Abstract
The interaction between carbon nanotubes (CNTs) and biological molecules of diagnostic and therapeutic interest, as well as the internalization of the CNTs-biomolecules complexes in different types of cell, has been extensively studied due to the potential use of these nanocomplexes as multifunctional nanoplatforms in a great variety of biomedical applications. The effective use of these nanobiotechnologies requires broad multidisciplinary studies of biocompatibility, regarding, for example, the in vitro and in vivo nanotoxicological assays, the capacity to target specific cells and the evaluation of their biomedical potential. However, the first step to be reached is the careful obtainment of the nanoplatform and the understanding of the actual surface composition and structural integrity of the complex system. In this work, we show the detailed construction of a nanoplatform created by the noncovalent interaction between oxidized multi walled carbon nanotubes (MWCNTs) and a DNA aptamer targeting tumor cells. The excess free aptamer was removed by successive washes, revealing the actual surface of the nanocomplex. The MWCNT-aptamer interaction by π-stacking was evidenced and shown to contribute in obtaining a stable nanocomplex compatible with aqueous media having good cell viability. The nucleotide sequence of the aptamer remained intact after the functionalization, allowing its use in further studies of specificity and binding affinity and for the construction of functional nanoplatforms.
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Affiliation(s)
| | | | | | | | - João Paulo Coelho
- Centro de Desenvolvimento da Tecnologia Nuclear, 31270-901 Belo Horizonte, MG, Brazil
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Poudel L, Steinmetz NF, French RH, Parsegian VA, Podgornik R, Ching WY. Implication of the solvent effect, metal ions and topology in the electronic structure and hydrogen bonding of human telomeric G-quadruplex DNA. Phys Chem Chem Phys 2018; 18:21573-85. [PMID: 27425864 DOI: 10.1039/c6cp04357g] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We present a first-principles density functional study elucidating the effects of solvent, metal ions and topology on the electronic structure and hydrogen bonding of 12 well-designed three dimensional G-quadruplex (G4-DNA) models in different environments. Our study shows that the parallel strand structures are more stable in dry environments and aqueous solutions containing K(+) ions within the tetrad of guanine but conversely, that the anti-parallel structure is more stable in solutions containing the Na(+) ions within the tetrad of guanine. The presence of metal ions within the tetrad of the guanine channel always enhances the stability of the G4-DNA models. The parallel strand structures have larger HOMO-LUMO gaps than antiparallel structures, which are in the range of 0.98 eV to 3.11 eV. Partial charge calculations show that sugar and alkali ions are positively charged whereas nucleobases, PO4 groups and water molecules are all negatively charged. Partial charges on each functional group with different signs and magnitudes contribute differently to the electrostatic interactions involving G4-DNA and favor the parallel structure. A comparative study between specific pairs of different G4-DNA models shows that the Hoogsteen OH and NH hydrogen bonds in the guanine tetrad are significantly influenced by the presence of metal ions and water molecules, collectively affecting the structure and the stability of G4-DNA.
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Affiliation(s)
- Lokendra Poudel
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA.
| | - Nicole F Steinmetz
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Radiology, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Materials Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Roger H French
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Materials Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - V Adrian Parsegian
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Rudolf Podgornik
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003, USA and Department of Theoretical Physics, J. Stefan Institute, SI-1000 Ljubljana, Slovenia and Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA.
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Adhikari P, Khaoulaf R, Ez-Zahraouy H, Ching WY. Complex interplay of interatomic bonding in a multi-component pyrophosphate crystal: K 2Mg (H 2P 2O 7) 2·2H 2O. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170982. [PMID: 29308239 PMCID: PMC5750006 DOI: 10.1098/rsos.170982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/30/2017] [Indexed: 06/07/2023]
Abstract
The electronic structure and interatomic bonding of pyrophosphate crystal K2Mg (H2P2O7)2·2H2O are investigated for the first time showing complex interplay of different types of bindings. The existing structure from single-crystal X-ray diffraction is not sufficiently refined, resulting in unrealistic short O─H bonds which is rectified by high-precision density functional theory (DFT) calculation. K2Mg (H2P2O7)2·2H2O has a direct gap of 5.22 eV and a small electron effective mass of 0.14 me. Detailed bond analysis between every pair of atoms reveals the complexity of various covalent, ionic, hydrogen bonding and bridging bonding and their sensitive dependence on structural differences. The K--O bonds are much weaker than Mg--O bonds and contributions from the hydrogen bonds are non-negligible. Quantitative analysis of internal cohesion in terms of total bond order density and partial bond order density divulges the relative importance of different types of bonding. The calculated optical absorptions show multiple peaks and a sharp Plasmon peak at 23 eV and a refractive index of 1.44. The elastic and mechanical properties show features unique to this low-symmetry crystal. Phonon calculation gives vibrational frequencies in agreement with reported Raman spectrum. These results provide new insights indicating that acidic pyrophosphates could have a variety of unrealized applications in advanced technology.
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Affiliation(s)
- Puja Adhikari
- Department of Physics and Astronomy, University of Missouri Kansas City, Kansas City, MO 64110, USA
| | - Redouane Khaoulaf
- Department of Physics, Laboratory of Optoelectronics and Physical Chemistry of Materials, Faculty of Sciences, University lbn Tofail, Kenitra, Morocco
- Laboratory of Condensed Matter and Interdisciplinary Sciences (LAMCSCI), Faculty of Sciences, University Mohammed V, Rabat, Morocco
| | - Hamid Ez-Zahraouy
- Laboratory of Condensed Matter and Interdisciplinary Sciences (LAMCSCI), Faculty of Sciences, University Mohammed V, Rabat, Morocco
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri Kansas City, Kansas City, MO 64110, USA
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8
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Arasu V, Dugasani SR, Kesama MR, Chung HK, Park SH. Luminophore Configuration and Concentration-Dependent Optoelectronic Characteristics of a Quantum Dot-Embedded DNA Hybrid Thin film. Sci Rep 2017; 7:11567. [PMID: 28912561 PMCID: PMC5599517 DOI: 10.1038/s41598-017-11797-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/31/2017] [Indexed: 11/29/2022] Open
Abstract
To be useful in optoelectronic devices and sensors, a platform comprising stable fluorescence materials is essential. Here we constructed quantum dots (QDs) embedded DNA thin films which aims for stable fluorescence through the stabilization of QDs in the high aspect ratio salmon DNA (SDNA) matrix. Also for maximum luminescence, different concentration and configurations of core- and core/alloy/shell-type QDs were embedded within SDNA. The QD-SDNA thin films were constructed by drop-casting and investigated their optoelectronic properties. The infrared, UV-visible and photoluminescence (PL) spectroscopies confirm the embedment of QDs in the SDNA matrix. Absolute PL quantum yield of the QD-SDNA thin film shows the ~70% boost due to SDNA matrix compared to QDs alone in aqueous phase. The linear increase of PL photon counts from few to order of 5 while increasing [QD] reveals the non-aggregation of QDs within SDNA matrix. These systematic studies on the QD structure, absorbance, and concentration- and thickness-dependent optoelectronic characteristics demonstrate the novel properties of the QD-SDNA thin film. Consequently, the SDNA thin films were suggested to utilize for the generalised optical environments, which has the potential as a matrix for light conversion and harvesting nano-bio material as well as for super resolution bioimaging- and biophotonics-based sensors.
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Affiliation(s)
- Velu Arasu
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Korea
| | - Sreekantha Reddy Dugasani
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Korea.,Department of Physics, Sungkyunkwan University, Suwon, 16419, Korea
| | | | - Ho Kyoon Chung
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Korea.
| | - Sung Ha Park
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Korea. .,Department of Physics, Sungkyunkwan University, Suwon, 16419, Korea.
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Marafon G, Menegazzo I, De Zotti M, Crisma M, Toniolo C, Moretto A. Tuning morphological architectures generated through living supramolecular assembly of a helical foldamer end-capped with two complementary nucleobases. SOFT MATTER 2017; 13:4231-4240. [PMID: 28509927 DOI: 10.1039/c7sm00764g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Two appropriately functionalized nucleobases, thymine and adenine, have been covalently linked at the N- and C-termini, respectively, of two α-aminoisobutyric acid-rich helical peptide foldamers, aiming at driving self-assembly through complementary recognition. A crystal-state analysis (by X-ray diffraction) on the shorter, achiral foldamer 1 unambiguously shows that adeninethymine base pairing, through Watson-Crick intermolecular H-bonding, does take place between either end of each peptide molecule. In the crystals, π-stacking between base pairs is also observed. Evidence for time-dependent foldameroldamer associations for the longer, chiral foldamer 2 in solution is provided by circular dichroism measurements. The self-assembly of foldamer 2, through living supramolecular polymerization, eventually leads to the formation of twisted fibers. Such a supramolecular organization can be affected by addition of either pristine adenine or thymine, that acts as a "terminator" by selectively matching a pairing nucleobase at one end of the foldamer. The co-assembly of foldamer 2 with a porphyrin-derivatized thymine, under appropriate experimental conditions, leads to the formation of vesicles which, in turn, can be converted to the fiber morphology by changing the environmental polarity. Conversely, dendrimeric, star polymer-like microstructures are generated when the supramolecular assembly of foldamer 2 is seeded by adenine-capped gold nanoparticles.
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Affiliation(s)
- Giulia Marafon
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.
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Gong Y, Adhikari P, Liu Q, Wang T, Gong M, Chan WL, Ching WY, Wu J. Designing the Interface of Carbon Nanotube/Biomaterials for High-Performance Ultra-Broadband Photodetection. ACS APPLIED MATERIALS & INTERFACES 2017; 9:11016-11024. [PMID: 28263551 DOI: 10.1021/acsami.7b00352] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Inorganic/biomolecule nanohybrids can combine superior electronic and optical properties of inorganic nanostructures and biomolecules for optoelectronics with performance far surpassing that achievable in conventional materials. The key toward a high-performance inorganic/biomolecule nanohybrid is to design their interface based on the electronic structures of the constituents. A major challenge is the lack of knowledge of most biomolecules due to their complex structures and composition. Here, we first calculated the electronic structure and optical properties of one of the cytochrome c (Cyt c) macromolecules (PDB ID: 1HRC ) using ab initio OLCAO method, which was followed by experimental confirmation using ultraviolet photoemission spectroscopy. For the first time, the highest occupied molecular orbital and lowest unoccupied molecular orbital energy levels of Cyt c, a well-known electron transport chain in biological systems, were obtained. On the basis of the result, pairing the Cyt c with semiconductor single-wall carbon nanotubes (s-SWCNT) was predicted to have a favorable band alignment and built-in electrical field for exciton dissociation and charge transfer across the s-SWCNT/Cyt c heterojunction interface. Excitingly, photodetectors based on the s-SWCNT/Cyt c heterojunction nanohybrids demonstrated extraordinary ultra-broadband (visible light to infrared) responsivity (46-188 A W-1) and figure-of-merit detectivity D* (1-6 × 1010 cm Hz1/2 W-1). Moreover, these devices can be fabricated on transparent flexible substrates by a low-lost nonvacuum method and are stable in air. These results suggest that the s-SWCNT/biomolecule nanohybrids may be promising for the development of CNT-based ultra-broadband photodetectors.
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Affiliation(s)
- Youpin Gong
- Department of Physics and Astronomy, University of Kansas , Lawrence, Kansas 66045, United States
- College of Physics, Optoelectronics and Energy, Key Lab of Advanced Optical Manufacturing Technologies of Jiangsu Province, and Key Lab of Modern Optical Technologies of Education Ministry of China, Soochow University , Suzhou 215006, China
| | - Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City , Kansas City, Missouri 64110, United States
| | - Qingfeng Liu
- Department of Physics and Astronomy, University of Kansas , Lawrence, Kansas 66045, United States
| | - Ti Wang
- Department of Physics and Astronomy, University of Kansas , Lawrence, Kansas 66045, United States
| | - Maogang Gong
- Department of Physics and Astronomy, University of Kansas , Lawrence, Kansas 66045, United States
| | - Wai-Lun Chan
- Department of Physics and Astronomy, University of Kansas , Lawrence, Kansas 66045, United States
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City , Kansas City, Missouri 64110, United States
| | - Judy Wu
- Department of Physics and Astronomy, University of Kansas , Lawrence, Kansas 66045, United States
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Sun H, Zhang S, Zhong C, Sun Z. Theoretical study of excited states of DNA base dimers and tetramers using optimally tuned range-separated density functional theory. J Comput Chem 2015; 37:684-93. [DOI: 10.1002/jcc.24266] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Haitao Sun
- State Key Laboratory of Precision Spectroscopy, Department of Physics; East China Normal University; Shanghai 200062 People's Republic of China
| | - Shian Zhang
- State Key Laboratory of Precision Spectroscopy, Department of Physics; East China Normal University; Shanghai 200062 People's Republic of China
| | - Cheng Zhong
- Department of Chemistry; Wuhan University; Hubei 430072 People's Republic of China
| | - Zhenrong Sun
- State Key Laboratory of Precision Spectroscopy, Department of Physics; East China Normal University; Shanghai 200062 People's Republic of China
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12
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Lu BS, Naji A, Podgornik R. Molecular recognition by van der Waals interaction between polymers with sequence-specific polarizabilities. J Chem Phys 2015; 142:214904. [DOI: 10.1063/1.4921892] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Bing-Sui Lu
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska ulica 19, SI-1000 Ljubljana, Slovenia
| | - Ali Naji
- School of Physics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran
| | - Rudolf Podgornik
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska ulica 19, SI-1000 Ljubljana, Slovenia
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